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Author : Tatiana Pimenova
Publisher :
ISBN 13 :
Total Pages : 147 pages
Book Rating : 4.:/5 (73 download)
Download or read book Probing Protein-protein Interactions by Mass Spectrometry written by Tatiana Pimenova and published by . This book was released on 2009 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andreas Barth
Publisher : IOS Press
ISBN 13 : 1607500450
Total Pages : 448 pages
Book Rating : 4.6/5 (75 download)
Download or read book Biological and Biomedical Infrared Spectroscopy written by Andreas Barth and published by IOS Press. This book was released on 2009 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although infrared spectroscopy has been applied with success to the study of important biological and biomedical processes for many years, key advances in this vibrant technique have led to its increasing use, ranging from characterization of individual macromolecules (DNA, RNA, lipids, proteins) to human tissues, cells and their components. Infrared spectroscopy thus has a significant role to play in the analysis of the vast number of genes and proteins being identified by the various genomic sequencing projects. Whilst this book gives an overview of the field, it highlights more recent developments, such as the use of bright synchrotron radiation for recording infrared spectra, the development of two-dimensional infrared spectroscopy and the ability to record infrared spectra at ultra fast speeds.
Author : Kevin Downard
Publisher : John Wiley & Sons
ISBN 13 : 047014632X
Total Pages : 153 pages
Book Rating : 4.4/5 (71 download)
Download or read book Mass Spectrometry of Protein Interactions written by Kevin Downard and published by John Wiley & Sons. This book was released on 2007-08-24 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authoritative guide to analyzing protein interactions by mass spectrometry Mass spectrometry (MS) is playing an increasingly important role in the study of protein interactions. Mass Spectrometry of Protein Interactionspresents timely and definitive discussions of the diverse range of approaches for studying protein interactions by mass spectrometry with an extensive set of references to the primary literature. Each chapter is written by authors or teams of authors who are international authorities in their fields. This leading reference text: * Discusses the direct detection of protein interactions through electrospray ionization (ESI-MS); ion mobility analysis; and matrix-assisted laser desorption/ionization (MALDI-MS) * Covers the indirect analysis of protein interactions through hydrogen-deuterium exchange (HX-MS); limited proteolysis; cross-linking; and radial probe (RP-MS) * Guides researchers in the use of mass spectrometry in structural biology, biochemistry, and protein science to map and define the huge number and diversity of protein interactions * Reviews the latest discoveries and applications and addresses new and ongoing challenges This is a comprehensive reference for researchers in academia and industry engaged in studies of protein interactions and an excellent text for graduate and postgraduate students.
Author :
Publisher :
ISBN 13 :
Total Pages : 640 pages
Book Rating : 4.:/5 (659 download)
Download or read book PROBING GAS-PHASE PEPTIDE STRUCTURE AND PROTEIN-PROTEIN INTERACTIONS USING MASS SPECTROMETRIC TECHNIQUES. written by and published by . This book was released on 2009 with total page 640 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presented in this dissertation are studies on the gas-phase structural features of peptides and peptide fragment ions using mass spectrometry (MS), hydrogen/deuterium (H/D) exchange, infrared multiphoton dissociation (IRMPD) spectroscopy, and computational modeling. Additional studies are presented on the mechanism of hydrogen/deuterium exchange using a model amino acid system. The application of chemical cross-linking to investigate the interaction between two proteins, LexA and RecA, is also presented. Gas-phase structural features can be probed using a number of techniques, and several of the studies presented in this dissertation involve the use of gas-phase H/D exchange. Although the basic mechanism for exchange has been determined, the factors that affect the rate and extent of exchange are not well understood. A computational modeling study of the exchange behavior of asparagine and its methyl ester demonstrated that exchange will occur preferentially at sites of more similar basicity. The distinctive exchange behavior of a model histidine-containing pentapeptide, HAAAA, prompted further studies into the structural features that result in five fast exchanging hydrogens and one slower exchange. Peptide analogues were used to identify the sites of exchange, and IRMPD spectroscopy combined with computational modeling indicated that exchange may occur because interaction with water at those sites results in lower energy structures compared to the other sites. Structural studies were also performed to determine whether the b2+ion from HAAAA is an oxazolone or diketopiperazine. The IRMPD spectrum showed bands that matched both a diketopiperazine and an oxazolone structure. H/D exchange and fragmentation studies further supported the presence of a mixture of species. Protein-protein interactions perform a vital role in regulating cellular processes. Despite extensive mutational analysis, the binding interaction between LexA and RecA, two proteins involved in the SOS response, is unclear. Chemical cross-linking experiments were undertaken to help target future mutational studies, and these studies identified two possible interactions. The first potential binding interaction is located in the cleft of RecA, and the second interaction may be caused by a LexA dimer binding across the RecA helical groove. The presence of two different binding interactions suggests that LexA may have redundant binding modes for RecA interaction.
Author : Stefan Theo Esswein
Publisher :
ISBN 13 :
Total Pages : 220 pages
Book Rating : 4.:/5 (781 download)
Download or read book Probing Protein-ligand Interactions Via Solution Phase Hydrogen Exchange Mass Spectrometry written by Stefan Theo Esswein and published by . This book was released on 2010 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is a versatile, sensitive and fast technique with which to probe biophysical properties in biological systems and one of the most important analytical tools in the multidisciplinary field of proteomics. The study of nativestate proteins and their complexes in the gas-phase is well established and direct infusion electrospray ionisation mass spectrometry (DI-ESI-MS) techniques are becoming increasingly popular as a tool for screening and determining quantitative information on protein-protein and protein-ligand interactions. However, complexes retained by ESI-MS are not always representative of those in solution and care must be taken in interpreting purely gas-phase results. This thesis details modification and advancement of solution phase techniques devised by Gross et al. utilising ESI-MS and Fitzgerald et al. applying matrix assisted laser desorption ionisation (MALDI)-MS termed PLIMSTEX (protein-ligand interactions by mass spectrometry, titration and hydrogen-deuterium-exchange)[1] and SUPREX (Stability of unpurified proteins from rates of H/D exchange)[2] to quantify these interactions with regards to high throughput analysis. The first part of this thesis describes the different developmental stages of the devised HPLC-front ends and their optimisation with myoglobin and insulin. The successfully developed HPLC-front end in conjunction with PLIMSTEX and SUPREX and ESI-MS then gets tested with self expressed and purified cyclophilin A(CypA)- cyclosporin A (CsA) system, followed by a test screen with potential CypA binding ligands. Dissociation constants (Kd's) within one order of magnitude to reported values are determined. In the third part of this thesis the application of the devised ESI-SUPREX methodology has been applied to anterior gradient 2 (AGr2) and the factor H complement control proteins module 19-20 (fH19-20) exhibiting binding potential to a taggedhexapeptide and a synthetic pentasaccharide, respectively, resulting in thermodynamical data for these protein-ligand interactions. For the AGr2 system another dimension of investigation has been added by temperature controlling the devised ESI-SUPREX approach, revealing a phase transition in the protein at higher temperatures. The final part of this thesis describes the application of the ESI-SUPREX methodology to probe folding properties of CypA in the presence of the self expressed and purified E. coli chaperonin groEL. Thereby the denaturing properties of groEL have been emphasised along with the stabilisation of a denatured CypA species.
Download or read book Probing Protein-protein Interactions with Peptide Libraries and Arrays written by and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Eugen Netz
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (14 download)
Download or read book Improved Cross-linking Mass Spectrometry Algorithms for Probing Protein Structures and Interactions written by Eugen Netz and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Carrie A. Hughes
Publisher :
ISBN 13 :
Total Pages : 320 pages
Book Rating : 4.:/5 (318 download)
Download or read book Protein-protein Interactions and Dynamics Probed by Hydrogen/deuterium Exchange written by Carrie A. Hughes and published by . This book was released on 2003 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Xudong Huang
Publisher :
ISBN 13 :
Total Pages : 196 pages
Book Rating : 4.:/5 (23 download)
Download or read book Probing Protein Conformation by Chemical Cross-linking and Mass Spectrometry written by Xudong Huang and published by . This book was released on 2004 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Timothy D. Veenstra
Publisher : John Wiley & Sons
ISBN 13 : 1119081696
Total Pages : 348 pages
Book Rating : 4.1/5 (19 download)
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2019-04-26 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: An update to the popular guide to proteomics technology applications in biomedical research Building on the strength of the original edition, this book presents the state of the art in the field of proteomics and offers students and scientists new tools and techniques to advance their own research. Written by leading experts in the field, it provides readers with an understanding of new and emerging directions for proteomics research and applications. Proteomics for Biological Discovery begins by discussing the emergence of proteomics technologies and summarizing the potential insights to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are thoroughly covered, from underlying concepts to limitations and future directions. Later chapters provide an overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, applied proteomics, and bioinformatics relevant to proteomics. Chapters cover: Quantitative Proteomics for Differential Protein Expression Profiling; Protein Microarrays; Protein Biomarker Discovery; Biomarker Discovery using Mass Spectrometry Imaging; Protein-Protein Interactions; Mass Spectrometry Of Intact Protein Complexes; Crosslinking Applications in Structural Proteomics; Functional Proteomics; High Resolution Interrogation of Biological Systems via Mass Cytometry; Characterization of Drug-Protein Interactions by Chemoproteomics; Phosphorylation; Large-Scale Phosphoproteomics; and Probing Glycoforms of Individual Proteins Using Antibody-Lectin Sandwich Arrays. Presents a comprehensive and coherent review of the major issues in proteomic technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Features new coverage of mass spectrometry for high throughput proteomic measurements, and novel quantitation strategies such as spectral counting and stable isotope labeling Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Offers new chapters on biomarker discovery, global phosphorylation analysis, proteomic profiling using antibodies, and single cell mass spectrometry Proteomics for Biological Discovery is an excellent advanced resource for graduate students, postdoctoral fellows, and scientists across all the major fields of biomedical science.
Author : Bingqing Zhao (Bioanalytical chemist)
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.5/5 (16 download)
Download or read book Advancing Chemical Cross-linking Mass Spectrometry for Protein Structure and Interaction Analysis written by Bingqing Zhao (Bioanalytical chemist) and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking mass spectrometry elucidates protein structures and protein-protein interactions by establishing distance constraints between residues pairs. Interpreting the mass spectra of covalently linked peptide pairs is more challenging than identifying peptides in proteomics. This dissertation presents improvements in methodology for identifying cross-linked peptides and their application to probing protein interacting surfaces.
Author : W. Andy Tao
Publisher : John Wiley & Sons
ISBN 13 : 1118970209
Total Pages : 448 pages
Book Rating : 4.1/5 (189 download)
Download or read book Mass Spectrometry-Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-31 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.
Author : Bich Thi Ngoc Vu
Publisher :
ISBN 13 :
Total Pages : 466 pages
Book Rating : 4.:/5 (174 download)
Download or read book Probing DNA Photoproduct Deamination Kinetics and DNA-binding Protein Interactions by Mass Spectrometry written by Bich Thi Ngoc Vu and published by . This book was released on 2007 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Haian Fu
Publisher : Springer Science & Business Media
ISBN 13 : 1592597629
Total Pages : 525 pages
Book Rating : 4.5/5 (925 download)
Download or read book Protein'Protein Interactions written by Haian Fu and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the mysteries stored in our DNA have been more completely revealed, scientists have begun to face the extraordinary challenge of unraveling the int- cate network of protein–protein interactions established by that DNA fra- work. It is increasingly clear that proteins continuously interact with one another in a highly regulated fashion to determine cell fate, such as proliferation, diff- entiation, or death. These protein–protein interactions enable and exert str- gent control over DNA replication, RNA transcription, protein translation, macromolecular assembly and degradation, and signal transduction; essentially all cellular functions involve protein–protein interactions. Thus, protein–p- tein interactions are fundamental for normal physiology in all organisms. Alt- ation of critical protein–protein interactions is thought to be involved in the development of many diseases, such as neurodegenerative disorders, cancers, and infectious diseases. Therefore, examination of when and how protein–p- tein interactions occur and how they are controlled is essential for understa- ing diverse biological processes as well as for elucidating the molecular basis of diseases and identifying potential targets for therapeutic interventions. Over the years, many innovative biochemical, biophysical, genetic, and computational approaches have been developed to detect and analyze p- tein–protein interactions. This multitude of techniques is mandated by the diversity of physical and chemical properties of proteins and the sensitivity of protein–protein interactions to cellular conditions.
Author : Weibo Cai
Publisher : BoD – Books on Demand
ISBN 13 : 9535103970
Total Pages : 488 pages
Book Rating : 4.5/5 (351 download)
Download or read book Protein-Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
Author :
Publisher :
ISBN 13 :
Total Pages : 434 pages
Book Rating : 4.:/5 (88 download)
Download or read book Chemistry for Probing Protein-protein Interactions written by and published by . This book was released on 2012 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most important tasks facing modern organic chemists is the development of new approaches to study the organic chemistry of living systems. One key aspect of this charge is to devise methods to probe and perturb the dynamic processes which are mediated by proteins. This thesis presents two distinct chemistry-based approaches for interrogating protein systems. Chemical approaches to protein modification can be used to install biophysical probes into proteins. We proposed to develop a bioconjugation reaction that could be used to modify proteins at a single residue. We recognized that L-pyrrolysine contained an electrophilic pyrroline moiety and, therefore, could be used as a reaction substrate for a chemoselective bioconjugation reaction. We have developed an efficient synthesis of pyrrolysine and generated pyrrolysine-containing proteins using the synthetically prepared amino acid. We explored its reactivity to small molecules containing activated esters. We discovered that, although pyrrolysine is reactive to nucleophiles, its ability to chemoselectively form stable adducts with a single reagent is elusive. By tuning the reactivity of the labeling reagent, we have identified a potential new class of pyrroline-reactive compounds. A second approach to characterizing protein systems is to introduce highly specific probes that interact with the protein complexes. We have prepared synthetic multivalent ligands to probe the organization of transmembrane protein clusters that Escherichia coli use to control their movement. The multivalent display of receptor-binding epitopes target specific receptors. A covalently-bound marker on the multivalent ligand can facilitate imaging of ligand-bound states of receptor clusters. Additionally, because whole cells can be difficult to image due to sample size, we have reconstituted the transmembrane proteins with their signaling partners in small vesicles and shown that they adopt native-like protein assemblies. We anticipate that the combined approach of multivalent reporter probes and reconstituted protein complexes in native membranes will lead to a molecular understanding of multi-protein oligomerization. Chemistry-based methods offer a unique approach for modifying protein structure while minimizing functional perturbations. By understanding chemical reactivity, the ability to synthesize large molecules and interrogate large protein complexes is not limited by the type, size or complexity of the materials at hand.
Author : Shahid Mukhtar
Publisher : Springer Nature
ISBN 13 : 1071633279
Total Pages : 480 pages
Book Rating : 4.0/5 (716 download)
Download or read book Protein-Protein Interactions written by Shahid Mukhtar and published by Springer Nature. This book was released on 2023-07-14 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides a comprehensive collection of classic and cutting-edge methods and techniques in mapping protein-protein interactions. The chapters include a variety of in vitro and in vivo experimental methods covering cell biology, biochemistry, and biophysics. In addition, the book also explores in silico methods including sequence-, structure-, and phylogenetic profile-based approaches as well as gene expression and machine learning methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein-Protein Interactions: Methods and Protocols serves as an ideal guide for researchers working in protein science and beyond.
